LAMMPS (18 Feb 2013)
# Simple rigid body system

units		lj
atom_style	atomic

pair_style	lj/cut 2.5

read_data	data.rigid
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 1 by 1 MPI processor grid
  81 atoms

velocity 	all create 100.0 4928459

# unconnected bodies

#group		clump1 id <> 1 9
#group		clump2 id <> 10 18
#group		clump3 id <> 19 27
#group		clump4 id <> 28 36
#group		clump5 id <> 37 45
#group		clump6 id <> 46 54
#group		clump7 id <> 55 63
#group		clump8 id <> 64 72
#group		clump9 id <> 73 81

#fix 1 all rigid group 9 clump1 clump2 clump3 clump4 clump5 #	  	      clump6 clump7 clump8 clump9

# 1 chain of connected bodies

#group		clump1 id <> 1 9
#group		clump2 id <> 9 18
#group		clump3 id <> 18 27
#group		clump4 id <> 27 36
#group		clump5 id <> 36 45
#group		clump6 id <> 45 54
#group		clump7 id <> 54 63
#group		clump8 id <> 63 72
#group		clump9 id <> 72 81

#fix 1 all poems group clump1 clump2 clump3 clump4 clump5 #	  	      clump6 clump7 clump8 clump9

# 2 chains of connected bodies

group		clump1 id <> 1 9
9 atoms in group clump1
group		clump2 id <> 9 18
10 atoms in group clump2
group		clump3 id <> 18 27
10 atoms in group clump3
group		clump4 id <> 27 36
10 atoms in group clump4
group		clump5 id <> 37 45
9 atoms in group clump5
group		clump6 id <> 45 54
10 atoms in group clump6
group		clump7 id <> 54 63
10 atoms in group clump7
group		clump8 id <> 63 72
10 atoms in group clump8
group		clump9 id <> 72 81
10 atoms in group clump9

fix 1 all poems group clump1 clump2 clump3 clump4
1 clusters, 4 bodies, 3 joints, 36 atoms
fix 2 all poems group clump5 clump6 clump7 clump8 clump9
1 clusters, 5 bodies, 4 joints, 45 atoms

neigh_modify	exclude group clump1 clump1
neigh_modify	exclude group clump2 clump2
neigh_modify	exclude group clump3 clump3
neigh_modify	exclude group clump4 clump4
neigh_modify	exclude group clump5 clump5
neigh_modify	exclude group clump6 clump6
neigh_modify	exclude group clump7 clump7
neigh_modify	exclude group clump8 clump8
neigh_modify	exclude group clump9 clump9

thermo		100

#dump		1 all atom 50 dump.rigid.poems2

#dump		1 all image 100 image.*.jpg type type #		axes yes 0.8 0.02 view 60 -30
#dump_modify	1 pad 5

timestep 	0.0001
thermo		50
run		10000
WARNING: More than one fix poems (fix_poems.cpp:332)
WARNING: More than one fix poems (fix_poems.cpp:332)
WARNING: One or more atoms are time integrated more than once (modify.cpp:220)
Memory usage per processor = 2.29003 Mbytes
Step Temp E_pair E_mol TotEng Press 
       0    196.00047    3632.2347            0    3668.5311   -2.7403788 
      50    12167.633    1505.5478            0    3758.8133    35.125973 
     100    17556.978    512.66277            0    3763.9549    11.137534 
     150    19579.586    138.04942            0    3763.8987   -29.953971 
     200     19757.51    105.30542            0    3764.1036 -0.030645317 
     250    18218.374    390.10747            0    3763.8804    13.711001 
     300    19383.039    174.40688            0    3763.8586    5.7240693 
     350    20125.986    36.972611            0    3764.0071    1.9559205 
     400    18888.816    266.10975            0    3764.0386    9.6362168 
     450    19307.656     188.2511            0     3763.743    1.9326206 
     500    16331.197    738.56392            0    3762.8597    9.1715579 
     550    19318.722    186.16172            0    3763.7027    3.0115336 
     600    19455.268    161.20621            0    3764.0336   0.55208034 
     650    18487.011    340.03216            0    3763.5528   -8.0359122 
     700    17321.201    556.32471            0    3763.9545   -13.631751 
     750    18979.187    249.04389            0    3763.7082   -2.6072455 
     800    19342.456    181.85552            0    3763.7918    8.1918726 
     850    19070.641    232.19342            0    3763.7936    7.3148472 
     900    19478.873    156.65987            0    3763.8586    2.4284987 
     950    19912.415    76.437437            0    3763.9216   -1.4667227 
    1000    16003.749    802.39753            0    3766.0548    46.642188 
    1050    19859.583     86.64176            0    3764.3424   -2.1961943 
    1100    19229.575    203.61488            0    3764.6473   -10.632365 
    1150      18821.6    279.15861            0      3764.64  -0.89495035 
    1200    19392.695    173.59744            0    3764.8373    1.8508753 
    1250    16459.624    717.32104            0    3765.3995    33.478127 
    1300    19343.863    182.59043            0    3764.7874   0.75890736 
    1350    20019.643    57.503573            0    3764.8448   0.31444672 
    1400    18549.582    329.31436            0    3764.4221    10.738303 
    1450    15163.926    957.47584            0    3765.6103   -17.923459 
    1500    19223.688    204.15169            0    3764.0939    -1.613454 
    1550    18147.996    404.12676            0    3764.8668    8.4194769 
    1600    18615.043    317.42464            0    3764.6548    -2.328898 
    1650    20120.654    38.887941            0     3764.935   -8.7620212 
    1700    19450.906    162.98296            0    3765.0025    2.3254683 
    1750    19374.633    177.37942            0    3765.2744    8.9328782 
    1800    19424.403    167.93976            0    3765.0514  0.081237835 
    1850    17936.373    442.81943            0    3764.3699    6.6007243 
    1900    19982.597    64.405942            0    3764.8868    -2.953039 
    1950    16216.047    761.87633            0     3764.848    13.993767 
    2000     18584.36     322.1319            0      3763.68    7.1655723 
    2050    20107.967    41.025515            0     3764.723  -0.31095875 
    2100    20002.359    60.588285            0    3764.7288   -6.7919218 
    2150    16949.463    626.65155            0    3765.4411    3.5099746 
    2200    20010.951    58.808709            0    3764.5403   -10.862337 
    2250    18982.724     247.0099            0    3762.3292  -0.53785372 
    2300    18401.404    354.86011            0    3762.5276    1.0917872 
    2350    19390.477    172.95029            0    3763.7793   -3.3527625 
    2400    16082.495    786.07427            0    3764.3141   -16.195237 
    2450    18871.033    268.63511            0    3763.2709    11.187102 
    2500     19687.13    117.79738            0    3763.5622    4.3929264 
    2550    18873.431    268.30382            0    3763.3836   -5.6531376 
    2600    17014.989    612.51599            0      3763.44    6.3265978 
    2650    18779.234    286.24534            0    3763.8812    2.3814839 
    2700    19733.494    108.84054            0    3763.1912  -0.28455721 
    2750    19487.299    154.68388            0    3763.4429   -1.5938513 
    2800    18419.252    351.12627            0    3762.0988    20.847774 
    2850    18788.886    283.58089            0    3763.0043    3.0280372 
    2900    20110.801    39.005938            0    3763.2284 0.0030136934 
    2950    15582.268    877.76573            0    3763.3708    16.827059 
    3000    17927.524    442.93443            0    3762.8463    4.0702273 
    3050    19054.272    234.78929            0    3763.3582    7.6784952 
    3100    19318.656    185.86832            0    3763.3972    3.4909968 
    3150    19336.244    182.13325            0    3762.9192    -19.24283 
    3200    18983.457    247.36835            0    3762.8233   -5.7526831 
    3250    19674.232    119.66794            0    3763.0442    1.9423166 
    3300    16157.209    769.95841            0    3762.0342      2.80189 
    3350    19030.029    239.07461            0    3763.1541    7.0444034 
    3400    15352.517    920.23705            0    3763.2957    26.469475 
    3450    19113.998    223.38478            0    3763.0139    5.4622379 
    3500    15355.047    921.10005            0    3764.6272    12.744088 
    3550    18453.302    345.84221            0    3763.1203    4.3303151 
    3600    15805.132    835.73363            0    3762.6098   -19.192108 
    3650    19366.655    176.75046            0     3763.168    3.6029674 
    3700    17926.815    443.58998            0    3763.3705    6.3106911 
    3750    18145.089    402.96409            0    3763.1657   -1.4495144 
    3800    17128.054    590.66146            0    3762.5233    1.3740587 
    3850    19650.661    123.98432            0    3762.9956   -3.6403709 
    3900    13651.635    1236.4269            0    3764.5075    1.8197344 
    3950    19607.542    131.80571            0    3762.8321   -5.2300693 
    4000    15976.222     803.9711            0    3762.5308    5.8844711 
    4050    17251.262    568.38221            0    3763.0604   -27.565001 
    4100    18718.869     296.1222            0    3762.5795   0.24957933 
    4150    18981.941    247.56533            0    3762.7396    8.9334676 
    4200    18058.249    418.65815            0    3762.7784   -9.7406053 
    4250     17840.27     458.9852            0    3762.7389   -1.2566229 
    4300    16801.487    651.25038            0    3762.6368    20.311604 
    4350    19284.648     191.5548            0     3762.786    3.8849247 
    4400    18089.637     412.4593            0     3762.392  -0.16156227 
    4450    18109.553    409.19646            0    3762.8174   -6.6744782 
    4500    18559.157    325.84529            0    3762.7262   -3.7834397 
    4550    19417.817     167.1903            0    3763.0824   -1.9438809 
    4600    19940.102    70.544215            0    3763.1558   -6.5714777 
    4650    17531.219    516.03395            0    3762.5561    16.825376 
    4700     18330.28    368.15762            0    3762.6539   -5.8154827 
    4750     18059.26    418.88115            0    3763.1886    6.9154907 
    4800    18230.172    387.09769            0    3763.0554   -5.8764301 
    4850    15352.316    920.35111            0    3763.3726   -14.150721 
    4900    17901.178    447.18401            0     3762.217    12.995669 
    4950    17096.795    596.75363            0    3762.8268    6.9584988 
    5000    18233.348    386.97511            0     3763.521   -8.6953829 
    5050    19238.643    200.76564            0    3763.4773  -0.95923788 
    5100    18851.592    272.21836            0    3763.2539    6.6015785 
    5150    17618.203     500.9924            0    3763.6226    6.4089848 
    5200    19510.809    150.29265            0    3763.4053    -1.138488 
    5250    17991.038    431.73878            0    3763.4124    0.9206177 
    5300    16496.992    709.42568            0    3764.4241     8.328767 
    5350     16683.15    674.66196            0    3764.1342   -12.119189 
    5400    19197.624    208.27759            0    3763.3932    1.8895925 
    5450    16776.936    656.25236            0    3763.0923    8.3324322 
    5500    18314.437    372.39317            0    3763.9556   0.87158511 
    5550    18678.675    304.31808            0    3763.3319    8.1494425 
    5600    18772.959    286.93218            0     3763.406   -1.3023432 
    5650    15494.947    894.36223            0    3763.7968   -10.336527 
    5700    18507.481    336.45923            0    3763.7704   -3.8746687 
    5750    17082.667    600.40729            0    3763.8641    42.148906 
    5800    19845.873    88.449333            0     3763.611    1.7380604 
    5850    17992.679    431.95872            0    3763.9363   -12.928704 
    5900    19680.707    119.00911            0    3763.5844  -0.79613571 
    5950    19914.393    75.816066            0    3763.6667    5.5342994 
    6000    19142.271    218.80112            0    3763.6661    7.4018805 
    6050    17025.724    611.14107            0     3764.053   -6.1043602 
    6100    18966.612    250.76138            0    3763.0969    1.1322144 
    6150     17451.81    531.32734            0     3763.144   -6.5894955 
    6200    16334.478     739.3296            0     3764.233   -27.518822 
    6250    18790.228    283.56338            0    3763.2353   -7.8911412 
    6300    18163.654    399.45237            0     3763.092  -0.20584174 
    6350     18674.03    305.36153            0    3763.5151    -10.44952 
    6400    19677.482     119.8165            0    3763.7947     4.767842 
    6450    19606.353    133.20697            0    3764.0132    3.1402747 
    6500    18685.174    303.25291            0    3763.4703     1.219211 
    6550    18842.997    274.29542            0    3763.7394   -3.0675196 
    6600    18984.844    247.94633            0    3763.6582    3.2871433 
    6650    19270.874    194.75275            0    3763.4332    2.0520948 
    6700     16730.98    665.42234            0     3763.752     24.63305 
    6750    18240.959    385.54575            0    3763.5012    9.3542656 
    6800    19212.072    205.42671            0    3763.2178   -4.7707967 
    6850    19428.264    165.41827            0    3763.2449   -5.9896144 
    6900    16510.385    705.90782            0    3763.3866   -4.5120114 
    6950    18469.724    342.72852            0    3763.0477    1.5930349 
    7000    19023.531    240.06714            0    3762.9432   0.97630625 
    7050     19981.38    63.051871            0    3763.3075    1.1975773 
    7100    18884.497     266.0407            0    3763.1698     5.014732 
    7150    20007.363    58.305336            0    3763.3725   -3.8475432 
    7200    19060.008    233.74726            0    3763.3784    -7.355987 
    7250    19587.118    136.14609            0    3763.3902 -0.071525055 
    7300     18255.08     382.9175            0    3763.4878    8.3070642 
    7350    19840.127    89.391828            0    3763.4894    3.0925365 
    7400    19081.218    229.96717            0    3763.5261 -0.088491483 
    7450    19495.919    153.12566            0     3763.481    7.3486168 
    7500    18103.878    410.89471            0    3763.4647     8.253657 
    7550    18818.034    278.46924            0    3763.2904   -6.6529064 
    7600    16900.909    634.03412            0    3763.8321    24.447016 
    7650    19309.193     187.4356            0    3763.2121    5.0831969 
    7700     17040.81    608.00812            0    3763.7136   -4.5789647 
    7750    19420.333    167.12363            0    3763.4815    4.3678178 
    7800    19164.248    214.10676            0    3763.0416   0.12405627 
    7850     19137.03    219.31269            0    3763.2071   -6.7131335 
    7900     19606.78    132.67382            0    3763.5591   -4.5096484 
    7950    18593.444    319.64585            0    3762.8763   -4.9001288 
    8000    19288.423    191.51728            0    3763.4475    3.8370068 
    8050     19132.57    220.46289            0    3763.5314   -1.3284232 
    8100    17510.857    520.52922            0    3763.2806   -4.6183989 
    8150    18356.887    364.17504            0    3763.5986    4.3938444 
    8200    19553.346    142.51623            0    3763.5063   0.93248057 
    8250    17919.922    444.70362            0    3763.2076    7.3984984 
    8300    17268.822    564.38824            0    3762.3182    24.155843 
    8350    19389.272    172.63516            0     3763.241    5.9225389 
    8400    17896.652    449.19012            0    3763.3849   0.63394353 
    8450    18315.977     371.4271            0    3763.2746   -33.234548 
    8500    16047.998    796.54623            0    3768.3978    51.901492 
    8550    19188.248    210.03454            0    3763.4138   -1.5401941 
    8600    17951.392    433.85317            0     3758.185    26.657038 
    8650    18678.909    304.65925            0    3763.7164   -0.5735548 
    8700    18473.965    342.61835            0    3763.7231  -0.39588258 
    8750    17278.537    562.78121            0    3762.5102    16.884408 
    8800    19997.623    60.585822            0    3763.8494   -2.7220886 
    8850    17720.683    482.98842            0    3764.5963    13.298184 
    8900    19450.503    162.05753            0    3764.0025   -5.0266355 
    8950    20065.748    48.178324            0    3764.0575    -3.298456 
    9000    18411.075    354.70332            0    3764.1617    2.5439463 
    9050    19835.128    90.878715            0    3764.0505   -2.4322016 
    9100    19486.363    155.54042            0    3764.1261    -5.332552 
    9150    19203.984    207.95102            0    3764.2443    3.1640673 
    9200    18048.222    421.26909            0    3763.5324    23.881772 
    9250    19682.985    119.25528            0    3764.2524     1.533906 
    9300    19857.159    86.947891            0    3764.1996   -4.5024234 
    9350    20060.359    49.452616            0    3764.3338    -1.493574 
    9400    19561.395    141.85818            0    3764.3387   -3.1573118 
    9450    19134.008    221.07861            0    3764.4133  -0.60832086 
    9500    18369.624    362.74228            0    3764.5244  -0.37049085 
    9550    18146.354    404.01981            0    3764.4558    10.150467 
    9600     15002.89    991.64237            0    3769.9553    51.550272 
    9650    18607.005    318.66284            0    3764.4045    3.3985276 
    9700    18489.496    340.51647            0    3764.4972     2.941698 
    9750    19635.157    128.29122            0    3764.4315   -14.101437 
    9800    18284.554       378.61            0    3764.6385   -7.2125841 
    9850    17756.297    476.00442            0    3764.2076   -4.4238573 
    9900    18996.512    246.68301            0    3764.5557   -5.0986512 
    9950    19432.438    165.78467            0    3764.3843   -3.7163888 
   10000    19336.629    183.60921            0    3764.4664  -0.93973872 
Loop time of 3.66627 on 1 procs for 10000 steps with 81 atoms

Pair  time (%) = 0.114009 (3.10966)
Neigh time (%) = 0.0713215 (1.94534)
Comm  time (%) = 0.0131958 (0.359923)
Outpt time (%) = 0.00205278 (0.055991)
Other time (%) = 3.4657 (94.5291)

Nlocal:    81 ave 81 max 81 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    69 ave 69 max 69 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    636 ave 636 max 636 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 636
Ave neighs/atom = 7.85185
Neighbor list builds = 991
Dangerous builds = 933
